chr19-48575967-G-A

Variant names:

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_177973.2(SULT2B1):c.98G>A(p.Arg33Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00363 in 1,613,454 control chromosomes in the GnomAD database, including 113 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0042 ( 23 hom., cov: 30)

Exomes 𝑓: 0.0036 ( 90 hom. )

Consequence

SULT2B1
NM_177973.2 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:2

Conservation

PhyloP100: -0.299

Variant links:

Genes affected

SULT2B1 (HGNC:11459): (sulfotransferase family 2B member 1) Sulfotransferase enzymes catalyze the sulfate conjugation of many hormones, neurotransmitters, drugs, and xenobiotic compounds. These cytosolic enzymes are different in their tissue distributions and substrate specificities. The gene structure (number and length of exons) is similar among family members. This gene sulfates dehydroepiandrosterone but not 4-nitrophenol, a typical substrate for the phenol and estrogen sulfotransferase subfamilies. Two alternatively spliced variants that encode different isoforms have been described. [provided by RefSeq, Jul 2008]

SULT2B1 links:

ENSG00000287603 (HGNC:):

ENSG00000287603 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0017948747).

BP6

Variant 19-48575967-G-A is Benign according to our data. Variant chr19-48575967-G-A is described in ClinVar as [Benign]. Clinvar id is 790920.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SULT2B1	NM_177973.2 link	c.98G>A	p.Arg33Gln	missense_variant	Exon 2 of 7	ENST00000201586.7	NP_814444.1	O00204-1
SULT2B1	NM_004605.2 link	c.53G>A	p.Arg18Gln	missense_variant	Exon 1 of 6		NP_004596.2	O00204-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
SULT2B1	ENST00000201586.7 link	c.98G>A	p.Arg33Gln	missense_variant	Exon 2 of 7	1	NM_177973.2	ENSP00000201586.2	O00204-1
SULT2B1	ENST00000323090.4 link	c.53G>A	p.Arg18Gln	missense_variant	Exon 1 of 6	1		ENSP00000312880.3	O00204-2
ENSG00000287603	ENST00000666424.1 link	n.493+20779C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.00420

AC:

639

AN:

152042

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000483

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000986

Gnomad ASJ

AF:

0.000577

Gnomad EAS

AF:

0.0778

Gnomad SAS

AF:

0.00579

Gnomad FIN

AF:

0.00396

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00179

Gnomad OTH

AF:

0.00288

GnomAD3 exomes

AF:

0.00761

AC:

1893

AN:

248884

Hom.:

AF XY:

0.00724

AC XY:

975

AN XY:

134732

show subpopulations

Gnomad AFR exome

AF:

0.000123

Gnomad AMR exome

AF:

0.000318

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0802

Gnomad SAS exome

AF:

0.00291

Gnomad FIN exome

AF:

0.00434

Gnomad NFE exome

AF:

0.00167

Gnomad OTH exome

AF:

0.00588

GnomAD4 exome

AF:

0.00357

AC:

5223

AN:

1461296

Hom.:

Cov.:

AF XY:

0.00350

AC XY:

2545

AN XY:

726902

show subpopulations

Gnomad4 AFR exome

AF:

0.000239

Gnomad4 AMR exome

AF:

0.000380

Gnomad4 ASJ exome

AF:

0.000115

Gnomad4 EAS exome

AF:

0.0564

Gnomad4 SAS exome

AF:

0.00301

Gnomad4 FIN exome

AF:

0.00521

Gnomad4 NFE exome

AF:

0.00181

Gnomad4 OTH exome

AF:

0.00668

GnomAD4 genome

AF:

0.00420

AC:

639

AN:

152158

Hom.:

Cov.:

AF XY:

0.00471

AC XY:

350

AN XY:

74386

show subpopulations

Gnomad4 AFR

AF:

0.000482

Gnomad4 AMR

AF:

0.000985

Gnomad4 ASJ

AF:

0.000577

Gnomad4 EAS

AF:

0.0780

Gnomad4 SAS

AF:

0.00580

Gnomad4 FIN

AF:

0.00396

Gnomad4 NFE

AF:

0.00179

Gnomad4 OTH

AF:

0.00285

Alfa

AF:

0.00399

Hom.:

Bravo

AF:

0.00434

TwinsUK

AF:

0.00189

AC:

ALSPAC

AF:

0.00156

AC:

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.00163

AC:

ExAC

AF:

0.00749

AC:

910

Asia WGS

AF:

0.0380

AC:

133

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

SULT2B1-related disorder

Benign:1

Aug 22, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

not provided

Benign:1

Jan 24, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.083

BayesDel_addAF

Benign

-0.63

BayesDel_noAF

Benign

-0.61

CADD

Benign

DANN

Benign

0.96

DEOGEN2

Benign

0.053

T;.

Eigen

Benign

-0.87

Eigen_PC

Benign

-0.75

FATHMM_MKL

Benign

0.13

LIST_S2

Benign

0.65

T;T

MetaRNN

Benign

0.0018

T;T

MetaSVM

Benign

-0.90

MutationAssessor

Benign

1.8

L;.

PrimateAI

Benign

0.24

PROVEAN

Benign

-0.16

N;N

REVEL

Benign

0.038

Sift

Benign

0.47

T;T

Sift4G

Benign

0.61

T;T

Polyphen

0.13

B;B

Vest4

0.11

MVP

0.082

MPC

0.32

ClinPred

0.0061

GERP RS

0.70

Varity_R

0.055

gMVP

0.54

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over